Biology subjects

Anderssen, S.

Publications and source records attributed to Anderssen, S..

4 recordsLinked to original sources

bioRxiv2026

Low intra-microbiota antagonism underlies stable and protective barley root microbiota

Plants rely on root-associated microbiota for growth and pathogen protection, yet the community properties underlying stable beneficial functions remain unclear. Here, we show that low intra-microbiota antagonism is associated with stability and pathogen protection in the barley root microbiota. Using a comprehensive culture collection of barley root endophytes, we reconstructed bacterial synthetic communities (SynComs) and compared a core SynCom resembling the natural microbiota with a trait-prioritized SynCom assembled from strains selected for predicted host benefits. Although strains from both communities exhibited broad pathogen-inhibitory potential, the communities behaved differently in planta. The core SynCom showed low internal antagonism, remained stable, and protected barley roots against fungal pathogens without impairing growth. In contrast, the trait-prioritized SynCom exhibited strong internal antagonism, unstable assembly, loss of protection, and reduced root growth. Together, our findings indicate that microbiota function cannot be predicted from individual strain traits alone. Rather, low intra-microbiota antagonism promotes community stability and enables protective functions to emerge in barley roots. Significance statementPlants rely on root microbiota for disease protection, yet the principles governing community stability and protective function remain poorly understood. Here, we show that low intra-microbiota antagonism is associated with a stable and protective barley root microbiota, whereas strong internal antagonism destabilizes communities, impairs root growth, and abolishes pathogen protection. These findings show that microbiota function depends not only on beneficial traits of individual strains, but also on compatibility among community members. HighlightsO_LILow intra-microbiota antagonism is associated with stable and protective barley root microbiota. C_LIO_LITrait-prioritized SynCom assembly with higher intra-microbiota antagonism can lead to dysbiosis. C_LIO_LIA highly antagonistic Pseudomonas strain is buffered by the core SynCom but detrimental in an unstable community. C_LIO_LICommunity compatibility better explains protection than individual strain traits. C_LIO_LIStable bacterial communities support fungal endophyte-mediated protection and maintain pathogen protection across barley genotypes. C_LI

plant biology↗

bioRxiv2022

AURTHO: autoregulation as facilitator of cis-acting element discovery of orthologous transcription factors

Transcriptional regulation is key in bacteria for providing an adequate response in time and space to changing environmental conditions. However, despite decades of research, the binding sites and therefore the target genes and the function of most transcription factors (TFs) remain unknown. Filling this gap in knowledge through conventional methods represents a colossal task which we demonstrate here can be significantly facilitated by a widespread feature in transcriptional control: the autoregulation of TFs implying that the yet unknown transcription factor binding site (TFBS) is neighbouring the TF itself. In this work, we describe the "AURTHO" methodology (AUtoregulation of oRTHOlogous transcription factors), consisting of analyzing upstream regions of orthologous TFs in order to uncover their associated TFBSs. AURTHO enabled the de novo identification of novel TFBSs with an unprecedented improvement in terms of quantity and reliability. DNA-protein interaction studies on a selection of candidate cis-acting elements yielded an >90% success rate, demonstrating the efficacy of AURTHO at highlighting true TF-TFBS couples and confirming the identification in a near future of a plethora of TFBSs across all bacterial species. Key pointsO_LITranscription factor (TF) autoregulation implies that their binding site (TFBS) is in their close vicinity C_LIO_LIWe developed and assessed the AURTHO methodology (AUtoregulation of oRTHOlogous TFs) for TFBS discovery C_LIO_LIOur results shows that AURTHO greatly facilitates the identification of highly reliable novel TFBSs C_LI

bioinformatics↗

bioRxiv2021

The virulome of Streptomyces scabiei in response to cello-oligosaccharides elicitors

2.The development of spots or lesions symptomatic of the common scab disease on root and tuber crops is caused by few pathogenic Streptomyces with Streptomyces scabiei 87-22 as the model species. Thaxtomin phytotoxins are the primary virulence determinants, mainly acting by impairing cellulose synthesis, and their production in S. scabiei is in turn boosted by the cello-oligosaccharides released from host plants. In this work we aimed to determine which molecules and which biosynthetic gene clusters (BGCs) of the specialized metabolism of S. scabiei 87-22 show a production and/or transcriptional response to cello-oligosaccharides. Comparative metabolomic and transcriptomic analyses revealed that molecules of the virulome of S. scabiei induced by cellobiose and cellotriose include i) thaxtomins and concanamycins phytotoxins (and to a lesser extent N-coronafacoyl-L-isoleucine), ii) desferrioxamines, scabichelin and turgichelin siderophores in order to acquire iron essential for housekeeping functions, iii) ectoine for protection against osmotic shock once inside the host, and iv) bottromycins and concanamycins antimicrobials possibly to prevent other microorganisms from colonizing the same niche. Importantly, both cell-oligosaccharides reduced the production of the spore germination inhibitors germicidins and the plant growth regulators rotihibins. The metabolomic study also revealed that cellotriose is in general a more potent elicitor of the virulome compared to cellobiose. This result supports an earlier hypothesis that suggested that the trisaccharide would be the real virulence-triggering factor released from the plant cell wall through the action of thaxtomins. Interestingly, except for thaxtomins, none of these BGCs expression seems to be under direct control of the cellulose utilization repressor CebR suggesting the existence of another master regulator sensing the internalization of cello-oligosaccharides. Finally, we found nine additional cryptic and orphan BGCs that have their expression awakened by cello-oligosaccharides, demonstrating that other and yet to be discovered metabolites are part of the virulome of S. scabiei. 3. Impact statementUnveiling the environmental triggers that signal proper conditions for host colonization and what is the composition of the arsenal of metabolites specialized for this task (the virulome) is key to understand host-pathogen interactions. In this work, focused on the induction of the common scab disease caused by Streptomyces species, we provided further knowledge to both aspects i.e., i) highlighting the capability of cellotriose to trigger the entire virulome and not only the production of thaxtomin phytotoxins, and ii) identifying the set of metabolites that specifically respond to cello-oligosaccharides emanating from the plant under attack. Importantly, we also revealed that the expression of nine cryptic/orphan biosynthetic gene clusters (BGCs) involved in the production of unknown compounds was drastically activated upon cello-oligosaccharides import suggesting that a significant part of the virulome of S. scabiei remains to be discovered. Finally, we unexpectedly found that the expression control of most of the known and cryptic BGCs does not depend on the cello-oligosaccharide utilization repressor CebR which suggests the existence of another and yet unknown master regulator of the virulence in S. scabiei. 4. Significance as a BioResource to the communityNot Applicable 5. OutcomeNot Applicable 6. Data summary[A section describing all supporting external data including the DOI(s) and/or accession numbers(s), and the associated URL.] The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. RNAseq data were publicly deposited, and our experimental and analytical pipeline were described on the GEO database repository (Accession number: GSE181490)

microbiology↗

bioRxiv2016

PREDetector 2.0: Online and Enhanced Version of the Prokaryotic Regulatory Elements Detector Tool

In the era that huge numbers of microbial genomes are being released in the databases, it becomes increasingly important to rapidly mine genes as well as predict the regulatory networks that control their expression. To this end, we have developed an improved and online version of the PREDetector software aimed at identifying putative transcription factor-binding sites (TFBS) in bacterial genomes. The original philosophy of PREDetector 1.0 is maintained, i.e. to allow users to freely fix the DNA-motif screening parameters, and to provide a statistical means to estimate the reliability of the prediction output. This new version offers an interactive table as well as graphics to dynamically alter the main screening parameters with automatic update of the list of identified putative TFBS. PREDetector 2.0 also has the following additional options: (i) access to genome sequences from different databases, (ii) access to weight matrices from public repositories, (iii) visualization of the predicted hits in their genomic context, (iv) grouping of hits identified in the same upstream region, (v) possibility to store the performed jobs, and (vi) automated export of the results in various formats. PREDetector 2.0 is available at http://predetector.fsc.ulg.ac.be/.

bioinformatics↗